8I0K

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase(E1) with TCAIM complex

• PDB DOI: https://doi.org/10.2210/pdb8I0K/pdb
• EM Map EMD-35042: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-11 Released: 2024-05-01 
• Deposition Author(s): Yu, X., Yang, W., Zhong, Y.H., Ma, X.M., Gao, Y.Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex

Yu, X., Yang, W., Zhong, Y.H., Ma, X.M., Gao, Y.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 243.96 kDa 
• Atom Count: 16,537 
• Modelled Residue Count: 2,052 
• Deposited Residue Count: 2,124 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate dehydrogenase complex component E1	A, B	911	Homo sapiens	Mutation(s): 0  Gene Names: OGDH EC: 1.2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02218 (Homo sapiens) Explore Q02218  Go to UniProtKB:  Q02218
PHAROS:  Q02218 GTEx:  ENSG00000105953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell activation inhibitor, mitochondrial	C	302	Homo sapiens	Mutation(s): 0  Gene Names: TCAIM, C3orf23, TOAG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3R3 (Homo sapiens) Explore Q8N3R3  Go to UniProtKB:  Q8N3R3
PHAROS:  Q8N3R3 GTEx:  ENSG00000179152

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8EL	G [auth B]	2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate C12 H20 N4 O7 P2 S FCUXBJDJFWOWMD-UHFFFAOYSA-N
TPP (Subject of Investigation/LOI)	E [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Yu, X., Yang, W., Zhong, Y.H., Ma, X.M., Gao, Y.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release